Lee Newberg Email & Phone Number

Albany, Ny, Us

Albany, Ny, Us

Clifton Park, New York, United States

Digital histopathology

Niskayuna, Ny

Employing R, UNIX for forensic protein fingerprinting bioinformatics. (Move over DNA fingerprinting!)• Created a panel of trypsin-digested peptides for identifying individuals, with strong random match probability, accommodating partial digests and combinatorial polymorphisms.

Malta, Ny

Employed Spark, R, Python, and SQL for big data statistics and analyses of transportation sector data.• Wrote software for efficiently and robustly ingesting the stream of traffic monitoring data. Provides quality checks, computes statistics, and organizes output into tables for subsequent users.• Designed database schema (Amazon Redshift) for traffic monitoring data. Provides database table normalizations and best practices for robustness and materialized views for typical use cases.

Niskayuna, Ny

Employed R, Python, Java, UNIX, and AWS to build software solutions for problems in bioinformatics. Specifically, analyzed NGS (high-throughput) DNA and RNA sequence data with existing software tools and novel algorithms, predominantly for cancer subtype identification. Conceived and deployed management plan for team data, software, and hardware, both locally and in the AWS cloud.• Greatly improved speed and accuracy of computational discovery of RNA expression biomarkers for differentiating cell types and normal and pathological cell states, by conceiving and deploying novel non-negative matrix factorization algorithm. Patent application filed.• Created and deployed algorithm for unsupervised detection of gene network modules important to cancer prognosis, from DNA somatic mutation data and RNA expression data. Provides genes whose RNA expression is a good proxy for underlying DNA damage in a gene module.• Created and deployed algorithm for optimizing DNA / codon sequence for a gene, leading to efficient protein production in GE proprietary protocol.• Debugged and maintained variant calling workflow for DNA sequence analysis of cancer, enabling colleagues to contribute significantly to projects.

Albany, Ny

Implemented software applications in C++ and UNIX for solving DNA sequence analysis problems. Specifically, computationally discovered transcription factor binding sites (TFBS), the portions of DNA sequence that play key role in activating or repressing nearby genes. Approaches include scanning for statistically significant instances of known TFBS motifs and identifying motifs de novo by their approximate conservation across multiple genes and multiple species. Also, Research Associate Professor of Computer Science at Rensselaer Polytechnic Institute, jointly.• Developed and implemented Bayesian model, algorithms, and software for identification of transcription factor binding sites from phylogenetically aligned, multi-species genomic sequence data, leading to discovery in data sets that were previous intractable.• Created and deployed algorithms to precisely compute small p-values using importance sampling, with 1st application to pairwise sequence alignment, providing evidence that discoveries are statistically significant in high-multiple-testing scenarios.• Designed and deployed algorithm for memory optimal backtracking through dynamic programming algorithm, permitting computation of optimal solutions when previously computation was too large to fit in computer memory.• Graduated 1 Ph.D. student in Computer Science. Secondary advisor / thesis committee for 5 students.• Principal investigator for funded grants from National Institutes of Health ($405K), National Science Foundation ($300K), Department of Energy ($199K), as well as co-PI / senior personnel on others.• Multiple 1st-author publications. Overall career: 20 published journal articles, 17 as 1st or co-1st author; see www.cs.rpi.edu/~leen/publications/.

Chicago, Il

Client-server model in C++ and UNIX. As an employee at Citadel, LLC and then as Founder and Managing Partner of Quant Consulting, LLC with Citadel as its primary customer, led quantitative analysis team responsible for merger arbitrage ("risk arb") portfolio of $2B. Familiarity with exotic financial derivatives.• Essential to profiting from many mergers and acquisitions by providing crucial accurate analytics within minutes of announced complex deal terms. These analytics allowed traders to compare likelihood of deal completion to real-time, hedgeable profit available.• Allowed traders to bypass need to work with me by continually expanding variety of deal terms supported by default from in-house analytics software tools.• Minimized effective exposure to foreign currency fluctuations by providing report tool to compute and monitor effective exposures.

Doctor Of Philosophy (Ph.D.), Computer Science, 4.0/4.0

Thesis: “Finding, Evaluating, and Counting DNA Physical Maps” with Richard M. Karp. National Science Foundation Graduate Fellowship.

Master’S Degree, Computer Science, 4.0/4.0

Thesis: “The k-Server Problem with Distinguishable Servers” with Richard M. Karp.

Bachelor’S Degree, Mathematics, 4.9/5.0 (5.0/5.0 In Mathematics, Physics, Computer Science.)

Also, BS Physics. Computational biology research with Eric S. Lander. Ranked #1 MIT Mathematics. Honorable mention (top 40) William Lowell.